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Sorry for being off-topic here, but I'm experiencing the same problem (luckily I do not need to profile a script which needs the bridge) - anyways - you mentioned in http://xdebug.org/archives/xdebug-general/1229.html that the usage of java.so is deprecated and that the development on the bridge is stalled. Since we've just started with a new project which uses the bridge, I'm a bit concerned about this comment actually - can you pinpoint me to a discussion or other ressource where you got these information?

Sorry for answering this late, Thomas.
Just to document this in case someone stumbles over this thread: the php-java-bridge is still under very active development as of today as one can easily see at the bridge's site at http://php-java-bridge.sourceforge.net/. I was just refering to the bridge's java.so which by now is no longer available.

I just had a chat with some of the other people that know the Zend Engine. Running zend_execute() from RINIT is never going to work reliably. As this is fixed in the java bridge, and you shouldn't do this anyway, I'm going to close this issue again.